It is implied that guards are able to do this through some text in game, though I'm not sure where (it was a book or a note or something). Aside from that, it would have been the perfect touch to the whale oil machine interaction. I always have a natural instinct to throw the tanks away in the water or drop them somewhere far off because I feel like the guards are able to put them back in if they notice the machine isn't working. I just really feel like that should have been a part of the gameplay and would have really helped it, though it's very good right now, too.
2) Enemies being able to wake up unconscious allies.
The guards say things like "Get up!" when they find their own allies sleeping, but there's never any actual waking them back up. They are essentially in a coma and it doesn't make much sense to me. Games like this often include the classic "If they find me sleeping they'll wake me up so you better hide me well" interaction, but it seems to be missing for no real reason.
3) Not being able to sell items.
I did my nonlethal playthrough yesterday, and this is a glaring omission. I have no use for grenades, spring razors, crossbow bolts, or pistol rounds. Why can't I sell them to buy some sleeping darts or upgrades? Also, the bolt capacity upgrades not applying to sleep darts is kind of weird.
Those are my issues with the game. I love it, but these things seem like they just didn't make it into the gameplay for no real reason.